Contacts of the helix formed by residues 547 - 562 (chain E) in PDB entry 6G52
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 547 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545E LYS* 4.1 2.0 + - - -
546E ILE* 1.3 78.1 - - - +
548E PRO* 1.3 75.4 - - - +
549E GLN* 4.4 3.4 - - - -
550E LEU* 3.4 11.2 + - - +
551E LEU* 3.3 18.5 + - - +
635G ALA* 4.4 13.7 + - - +
636G PHE* 3.5 30.0 - - - -
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Residues in contact with PRO 548 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546E ILE 4.3 2.2 - - - +
547E SER* 1.3 87.2 - - - +
549E GLN* 1.3 56.8 + - - +
551E LEU* 3.2 7.3 + - + +
552E LEU* 2.9 31.6 + - - +
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Residues in contact with GLN 549 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547E SER* 3.3 3.0 - - - +
548E PRO* 1.3 79.8 - - - +
550E LEU* 1.3 58.5 + - - +
552E LEU* 4.0 4.7 - - - +
553E ALA* 2.9 32.4 + - - +
553G ALA* 5.2 2.8 - - + +
557G PHE* 4.4 27.6 - - + -
636G PHE* 4.3 20.9 - - + -
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Residues in contact with LEU 550 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546E ILE* 5.5 4.7 - - + -
547E SER* 3.4 23.6 + - - +
548E PRO 3.3 0.4 - - - -
549E GLN* 1.3 78.0 - - - +
551E LEU* 1.3 58.5 + - - +
553E ALA* 3.6 4.5 + - - +
554E ALA* 2.9 29.5 + - - +
616E LEU* 5.0 8.4 - - + +
636E PHE* 4.3 6.0 - - + -
550G LEU* 5.9 3.6 - - + -
636G PHE* 4.0 16.2 - - + -
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Residues in contact with LEU 551 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546E ILE* 5.7 5.3 - - + +
547E SER 3.3 9.3 + - - +
548E PRO* 3.2 11.1 + - + +
550E LEU* 1.3 76.1 - - - +
552E LEU* 1.3 59.6 + - - +
554E ALA* 3.1 7.8 + - - +
555E HIS* 2.9 28.1 + - - +
579E LEU* 4.3 11.3 - - + +
585E ILE* 6.4 1.8 - - + -
616E LEU* 5.4 7.4 - - + -
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Residues in contact with LEU 552 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548E PRO 2.9 17.2 + - - +
549E GLN* 4.0 5.2 - - - +
551E LEU* 1.3 76.0 - - - +
553E ALA* 1.3 63.7 + - - +
555E HIS* 2.7 39.1 + - + -
556E ARG* 2.9 12.0 + - - +
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Residues in contact with ALA 553 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549E GLN 2.9 19.9 + - - +
550E LEU* 3.9 4.9 - - - +
552E LEU* 1.3 77.3 - - - +
554E ALA* 1.3 57.1 + - - +
556E ARG* 3.1 11.3 + - - +
557E PHE* 2.9 26.5 + - - +
636E PHE* 4.4 10.7 - - + -
549G GLN* 5.3 0.8 - - + +
553G ALA* 3.6 29.8 - - + -
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Residues in contact with ALA 554 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550E LEU 2.9 20.5 + - - +
551E LEU* 3.1 8.0 + - - +
553E ALA* 1.3 76.9 - - - +
555E HIS* 1.3 57.8 + - - +
557E PHE* 3.1 5.5 + - - +
558E LEU* 2.9 31.3 + - - +
579E LEU* 5.5 2.7 - - + -
614E LEU* 4.5 4.7 - - + -
616E LEU* 3.9 17.5 - - + -
636E PHE* 3.5 28.2 - - + -
709E ILE* 5.5 2.7 - - + -
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Residues in contact with HIS 555 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551E LEU 2.9 8.1 + - - +
552E LEU* 2.7 40.4 + - + -
554E ALA* 1.3 72.8 - - - +
556E ARG* 1.3 65.5 + - + +
558E LEU* 3.9 7.0 - - - +
559E ALA* 2.9 34.6 + - + +
572E GLU* 4.5 23.2 + - + +
575E LEU* 4.3 25.6 - - + +
576E LEU* 5.5 17.3 - - + +
579E LEU* 3.4 27.0 - - + +
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Residues in contact with ARG 556 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552E LEU 2.9 12.9 + - - +
553E ALA* 3.2 14.1 - - - +
555E HIS* 1.3 84.2 - - + +
557E PHE* 1.3 51.9 + - - +
559E ALA* 3.9 3.3 - - - +
560E THR* 2.7 45.5 + - + +
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Residues in contact with PHE 557 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553E ALA 2.9 12.2 + - - +
554E ALA* 3.1 9.2 + - - +
556E ARG* 1.3 77.2 - - - +
558E LEU* 1.3 59.9 + - - +
560E THR* 3.9 4.5 - - - -
561E GLU* 2.9 46.3 + - + +
562E VAL* 4.3 3.1 - - + -
614E LEU* 3.5 26.7 - - + -
636E PHE* 3.6 29.4 - + + -
638E TYR* 3.4 41.5 - + - -
549G GLN* 3.2 43.3 - - + -
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Residues in contact with LEU 558 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554E ALA 2.9 16.3 + - - +
555E HIS* 3.9 8.1 - - - +
556E ARG 3.3 0.2 - - - -
557E PHE* 1.3 75.6 - - - +
559E ALA* 1.3 63.3 + - - +
562E VAL* 3.3 25.5 + - + +
565E PHE* 3.2 55.1 - - + +
575E LEU* 4.5 9.0 - - + -
579E LEU* 4.6 10.1 - - + -
612E PHE* 3.8 21.8 - - + -
614E LEU* 3.5 25.4 - - + -
709E ILE* 3.7 29.6 - - + -
711E ILE* 5.4 0.2 - - + -
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Residues in contact with ALA 559 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555E HIS* 2.9 23.0 + - + +
556E ARG* 3.9 4.3 - - - +
558E LEU* 1.3 80.0 - - - +
560E THR* 1.3 66.4 + - + +
562E VAL 3.8 2.3 - - - +
565E PHE 3.6 12.8 - - - +
566E SER* 3.6 7.6 + - - -
567E PRO* 3.4 35.3 - - + +
575E LEU* 5.2 9.1 - - + +
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Residues in contact with THR 560 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556E ARG* 2.7 30.3 + - + +
557E PHE* 3.7 4.0 + - - -
559E ALA* 1.3 83.9 - - + +
561E GLU* 1.3 68.8 + - - +
562E VAL 3.5 2.3 + - - +
566E SER* 5.7 0.2 + - - -
567E PRO* 5.5 0.4 - - - -
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Residues in contact with GLU 561 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E PHE* 2.9 39.1 + - + +
560E THR* 1.3 81.1 + - - +
562E VAL* 1.3 64.4 + - - +
638E TYR* 3.9 14.1 + - + -
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Residues in contact with VAL 562 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557E PHE* 3.9 4.0 - - + +
558E LEU* 3.3 40.8 + - + +
559E ALA 3.8 3.8 - - - +
560E THR 3.4 2.7 - - - +
561E GLU* 1.3 85.4 - - - +
563E SER* 1.3 67.0 + - - +
564E GLN* 3.4 19.7 - - - +
565E PHE* 3.6 23.3 - - + -
566E SER* 3.1 20.0 + - - -
612E PHE* 5.6 1.3 - - + -
638E TYR* 3.9 27.8 - - + +
641E THR* 3.9 8.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il